Plot intensity of gain or loss
cnv_plot_intensity.RdThis function is used to represent gain or loss of copy number along the transcriptome. The purpose is then to identify regions carrying anomalies. Note that, even if losses are visualized, the intensity is a positive value.
Usage
cnv_plot_intensity(
table_cnv,
chr = NULL,
what = "gain",
log_scale = FALSE,
noise_thresh = 0.075,
contrib_fun = sum
)Arguments
- table_cnv
DATAFRAME : dataframe (genes x cells) containing CNV. Genes must be in the transcriptome order (no default).
- chr
VECTOR : a vector containing the chromosome for each gene. It must be the same length as rownames(table_cnv). If not provided, there will be no chromosome annotation (default to NULL)
- what
CHARACTER : either "gain" or "loss" (default to "gain")
- log_scale
LOGICAL : either to represent intensity in log scale or not (default to FALSE)
- noise_thresh
NUMERIC : a threshold above (or below) which a cell is said to carry an anomaly at a specific region. It is used to compute intensity. Value close to 0 will increase the background. It must be in range(table_cnv). If what = "gain", noise_thresh > 0, and if what = "loss", noise_thresh < 0 (default to 0.075)
- contrib_fun
FUNCTION : function to compute cells contribution to CNV. It could be sum, mean... of cells having a value above noise_thresh (default to sum)